Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2
Introduction: The ongoing coronavirus disease 2019 (COVID-19), which emerged in December 2019, is a serious health concern throughout the world. Despite massive COVID-19 vaccination on a global scale, there is a rising need to develop more effective vaccines and drugs to curb the spread of coronavir...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-10-01
|
| Series: | Vaccines |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-393X/10/10/1660 |
| _version_ | 1827647859274547200 |
|---|---|
| author | Shabir Ahmad Mir Mohammed Alaidarous Bader Alshehri Abdul Aziz Bin Dukhyil Saeed Banawas Yahya Madkhali Suliman A. Alsagaby Ayoub Al Othaim |
| author_facet | Shabir Ahmad Mir Mohammed Alaidarous Bader Alshehri Abdul Aziz Bin Dukhyil Saeed Banawas Yahya Madkhali Suliman A. Alsagaby Ayoub Al Othaim |
| author_sort | Shabir Ahmad Mir |
| collection | DOAJ |
| description | Introduction: The ongoing coronavirus disease 2019 (COVID-19), which emerged in December 2019, is a serious health concern throughout the world. Despite massive COVID-19 vaccination on a global scale, there is a rising need to develop more effective vaccines and drugs to curb the spread of coronavirus. Methodology: In this study, we screened the amino acid sequence of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 (the causative agent of COVID-19) for the identification of B and T cell epitopes using various immunoinformatic tools. These identified potent B and T cell epitopes with high antigenicity scores were linked together to design the multi-epitope vaccine construct. The physicochemical properties, overall quality, and stability of the designed vaccine construct were confirmed by suitable bioinformatic tools. Results: After proper in silico prediction and screening, we identified 3 B cell, 18 CTL, and 10 HTL epitopes from the RdRp protein sequence. The screened epitopes were non-toxic, non-allergenic, and highly antigenic in nature as revealed by appropriate servers. Molecular docking revealed stable interactions of the designed multi-epitope vaccine with human TLR3. Moreover, in silico immune simulations showed a substantial immunogenic response of the designed vaccine. Conclusions: These findings suggest that our designed multi-epitope vaccine possessing intrinsic T cell and B cell epitopes with high antigenicity scores could be considered for the ongoing development of peptide-based novel vaccines against COVID-19. However, further in vitro and in vivo studies need to be performed to confirm our in silico observations. |
| first_indexed | 2024-03-09T19:25:26Z |
| format | Article |
| id | doaj.art-f5bcb4e4a46549ba8dc70cab6f1d7670 |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-09T19:25:26Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-f5bcb4e4a46549ba8dc70cab6f1d76702023-11-24T03:03:50ZengMDPI AGVaccines2076-393X2022-10-011010166010.3390/vaccines10101660Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2Shabir Ahmad Mir0Mohammed Alaidarous1Bader Alshehri2Abdul Aziz Bin Dukhyil3Saeed Banawas4Yahya Madkhali5Suliman A. Alsagaby6Ayoub Al Othaim7Department of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaDepartment of Medical Laboratory Sciences, College of Applied Medical Science, Majmaah University, Al Majmaah 11952, Saudi ArabiaIntroduction: The ongoing coronavirus disease 2019 (COVID-19), which emerged in December 2019, is a serious health concern throughout the world. Despite massive COVID-19 vaccination on a global scale, there is a rising need to develop more effective vaccines and drugs to curb the spread of coronavirus. Methodology: In this study, we screened the amino acid sequence of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 (the causative agent of COVID-19) for the identification of B and T cell epitopes using various immunoinformatic tools. These identified potent B and T cell epitopes with high antigenicity scores were linked together to design the multi-epitope vaccine construct. The physicochemical properties, overall quality, and stability of the designed vaccine construct were confirmed by suitable bioinformatic tools. Results: After proper in silico prediction and screening, we identified 3 B cell, 18 CTL, and 10 HTL epitopes from the RdRp protein sequence. The screened epitopes were non-toxic, non-allergenic, and highly antigenic in nature as revealed by appropriate servers. Molecular docking revealed stable interactions of the designed multi-epitope vaccine with human TLR3. Moreover, in silico immune simulations showed a substantial immunogenic response of the designed vaccine. Conclusions: These findings suggest that our designed multi-epitope vaccine possessing intrinsic T cell and B cell epitopes with high antigenicity scores could be considered for the ongoing development of peptide-based novel vaccines against COVID-19. However, further in vitro and in vivo studies need to be performed to confirm our in silico observations.https://www.mdpi.com/2076-393X/10/10/1660COVID-19epitopeimmunoinformaticspeptide vaccineRNA polymeraseSARS-CoV-2 |
| spellingShingle | Shabir Ahmad Mir Mohammed Alaidarous Bader Alshehri Abdul Aziz Bin Dukhyil Saeed Banawas Yahya Madkhali Suliman A. Alsagaby Ayoub Al Othaim Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2 Vaccines COVID-19 epitope immunoinformatics peptide vaccine RNA polymerase SARS-CoV-2 |
| title | Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2 |
| title_full | Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2 |
| title_fullStr | Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2 |
| title_full_unstemmed | Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2 |
| title_short | Immunoinformatics-Based Identification of B and T Cell Epitopes in RNA-Dependent RNA Polymerase of SARS-CoV-2 |
| title_sort | immunoinformatics based identification of b and t cell epitopes in rna dependent rna polymerase of sars cov 2 |
| topic | COVID-19 epitope immunoinformatics peptide vaccine RNA polymerase SARS-CoV-2 |
| url | https://www.mdpi.com/2076-393X/10/10/1660 |
| work_keys_str_mv | AT shabirahmadmir immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT mohammedalaidarous immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT baderalshehri immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT abdulazizbindukhyil immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT saeedbanawas immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT yahyamadkhali immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT sulimanaalsagaby immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 AT ayoubalothaim immunoinformaticsbasedidentificationofbandtcellepitopesinrnadependentrnapolymeraseofsarscov2 |